major refactor of the code

27 files changed, 525 insertions, 270 deletions

diff --git a/include/gensvm_base.h b/include/gensvm_base.h
new file mode 100644
index 0000000..b1f4a6b
--- /dev/null
+++ b/include/gensvm_base.h
@@ -0,0 +1,116 @@
+/**
+ * @file gensvm_base.h
+ * @author Gertjan van den Burg
+ * @date May, 2016
+ * @brief Definitions for GenData and GenModel structures
+ *
+ * @details
+ * Contains documentation and declarations of GenModel and GenData.
+ *
+ */
+
+#ifndef GENSVM_BASE_H
+#define GENSVM_BASE_H
+
+// includes
+#include "globals.h"
+
+// type declarations
+
+/**
+ * @brief A structure to represent the data.
+ *
+ * @param K 		number of classes
+ * @param n 		number of instances
+ * @param m 		number of predictors
+ * @param *y 		pointer to vector of class labels
+ * @param *Z 		pointer to augmented data matrix
+ * @param *RAW 		pointer to augmented raw data matrix
+ * @param *J 		pointer to regularization vector
+ * @param kerneltype 	kerneltype used in GenData::Z
+ * @param *kernelparam 	kernel parameters used in GenData::Z
+ *
+ */
+struct GenData {
+	long K;
+	///< number of classes
+	long n;
+	///< number of instances
+	long m;
+	///< number of predictors (width of RAW)
+	long r;
+	///< number of eigenvalues (width of Z)
+ 	long *y;
+	///< array of class labels, 1..K
+	double *Z;
+	///< augmented data matrix (either equal to RAW or to the eigenvectors
+	///< of the kernel matrix)
+	double *RAW;
+	///< augmented raw data matrix
+	double *Sigma;
+	KernelType kerneltype;
+ 	double *kernelparam;
+};
+
+/**
+ * @brief A structure to represent a single GenSVM model.
+ *
+ */
+struct GenModel {
+	int weight_idx;
+	///< which weights to use (1 = unit, 2 = group)
+	long K;
+	///< number of classes in the dataset
+	long n;
+	///< number of instances in the dataset
+	long m;
+	///< number of predictor variables in the dataset
+	double epsilon;
+	///< stopping criterion for the IM algorithm.
+	double p;
+	///< parameter for the L-p norm in the loss function
+	double kappa;
+	///< parameter for the Huber hinge function
+	double lambda;
+	///< regularization parameter in the loss function
+	double *W;
+	///< weight matrix
+	double *t;
+	///< translation vector
+	double *V;
+	///< augmented weight matrix
+	double *Vbar;
+	///< augmented weight matrix from the previous iteration of the IM
+	///< algorithm
+	double *U;
+	///< simplex matrix
+	double *UU;
+	///< 3D simplex difference matrix
+	double *Q;
+	///< error matrix
+	double *H;
+	///< Huber weighted error matrix
+	double *R;
+	///< 0-1 auixiliary matrix, this matrix is n x K, with for row i a 0 on
+	///< column y[i]-1, and 1 everywhere else.
+	double *rho;
+	///< vector of instance weights
+	double training_error;
+	///< loss function value after training has finished
+	char *data_file;
+	///< filename of the data
+	KernelType kerneltype;
+	///< type of kernel used in the model
+	double *kernelparam;
+	///< array of kernel parameters, size depends on kernel type
+};
+
+// function declarations
+struct GenModel *gensvm_init_model();
+void gensvm_allocate_model(struct GenModel *model);
+void gensvm_reallocate_model(struct GenModel *model, long n, long m);
+void gensvm_free_model(struct GenModel *model);
+struct GenData *gensvm_init_data();
+void gensvm_free_data(struct GenData *data);
+
+#endif
diff --git a/include/gensvm_cmdarg.h b/include/gensvm_cmdarg.h
new file mode 100644
index 0000000..ac33be8
--- /dev/null
+++ b/include/gensvm_cmdarg.h
@@ -0,0 +1,21 @@
+/**
+ * @file gensvm_cmdarg.h
+ * @author Gertjan van den Burg
+ * @date May, 2016
+ * @brief Header file for gensvm_cmdarg.c
+ *
+ * @details
+ * Function declarations for dealing with command line arguments.
+ *
+ */
+
+#ifndef GENSVM_CMDARG_H
+#define GENSVM_CMDARG_H
+
+#include "globals.h"
+
+// function declarations
+int gensvm_check_argv(int argc, char **argv, char *str);
+int gensvm_check_argv_eq(int argc, char **argv, char *str);
+
+#endif
diff --git a/include/gensvm_copy.h b/include/gensvm_copy.h
new file mode 100644
index 0000000..bdf6eec
--- /dev/null
+++ b/include/gensvm_copy.h
@@ -0,0 +1,18 @@
+/**
+ * @file gensvm_copy.h
+ * @author Gertjan van den Burg
+ * @date May, 2016
+ * @brief Header file for gensvm_copy.c
+ *
+ */
+
+#ifndef GENSVM_COPY_H
+#define GENSVM_COPY_H
+
+// includes
+#include "gensvm_base.h"
+
+// function declarations
+void gensvm_copy_model(struct GenModel *from, struct GenModel *to);
+
+#endif
diff --git a/include/gensvm_crossval.h b/include/gensvm_cv_util.h
index 3ac5fa9..ada727d 100644
--- a/include/gensvm_crossval.h
+++ b/include/gensvm_cv_util.h
@@ -1,8 +1,8 @@
 /**
- * @file crossval.h
+ * @file gensvm_cv_util.h
  * @author Gertjan van den Burg
  * @date January, 2014
- * @brief Header file for crossval.c
+ * @brief Header file for gensvm_cv_util.c
  *
  * @details
  * Contains function declarations for functions needed for performing cross
@@ -10,11 +10,10 @@
  *
  */
 
-#ifndef GENSVM_CROSSVAL_H
-#define GENSVM_CROSSVAL_H
+#ifndef GENSVM_CV_UTIL_H
+#define GENSVM_CV_UTIL_H
 
-// forward delaration
-struct GenData;
+#include "gensvm_base.h"
 
 void gensvm_make_cv_split(long N, long folds, long *cv_idx);
 void gensvm_get_tt_split(struct GenData *full_data, struct GenData *train_data,
diff --git a/include/gensvm_debug.h b/include/gensvm_debug.h
new file mode 100644
index 0000000..1cab4ca
--- /dev/null
+++ b/include/gensvm_debug.h
@@ -0,0 +1,20 @@
+
+/**
+ * @file gensvm_debug.h
+ * @author Gertjan van den Burg
+ * @date May, 2016
+ * @brief Header for useful debug functions
+ *
+ * @details
+ * Contains defines useful for debugging.
+ *
+ */
+
+#ifndef GENSVM_DEBUG_H
+#define GENSVM_DEBUG_H
+
+#include "gensvm_print.h"
+
+void print_matrix(double *M, long rows, long cols);
+
+#endif
diff --git a/include/gensvm_grid.h b/include/gensvm_grid.h
new file mode 100644
index 0000000..d335d7c
--- /dev/null
+++ b/include/gensvm_grid.h
@@ -0,0 +1,78 @@
+/**
+ * @file gensvm_grid.h
+ * @author Gertjan van den Burg
+ * @date May, 2016
+ * @brief Structs necessary for the grid search
+ *
+ * @details
+ * The grid search for the optimal parameters is done through a queue.
+ * This file contains struct definitions for this queue and a single
+ * task in a queue, as well as a structure for the complete training
+ * scheme. Function declarations are also included.
+ *
+ */
+
+#ifndef GENSVM_GRID_H
+#define GENSVM_GRID_H
+
+#include "globals.h"
+
+/**
+ * @brief Structure for describing the entire grid search
+ *
+ * @param traintype 		type of training to use
+ * @param kerneltype 		type of kernel to use throughout training
+ * @param repeats 		number of repeats to be done after the grid
+ * 				search to find the parameter set with the
+ * 				most consistent high performance
+ * @param folds 		number of folds in cross validation
+ * @param Np 			size of the array of p values
+ * @param Nl 			size of the array of lambda values
+ * @param Nk 			size of the array of kappa values
+ * @param Ne 			size of the array of epsilon values
+ * @param Nw 			size of the array of weight_idx values
+ * @param Ng 			size of the array of gamma values
+ * @param Nc 			size of the array of coef values
+ * @param Nd 			size of the array of degree values
+ * @param *weight_idxs 		array of weight_idxs
+ * @param *ps 			array of p values
+ * @param *lambdas 		array of lambda values
+ * @param *kappas 		array of kappa values
+ * @param *epsilons 		array of epsilon values
+ * @param *gammas 		array of gamma values
+ * @param *coefs 		array of coef values
+ * @param *degrees 		array of degree values
+ * @param *train_data_file 	filename of train data file
+ * @param *test_data_file 	filename of test data file
+ *
+ */
+struct GenGrid {
+	TrainType traintype;
+	KernelType kerneltype;
+	long repeats;
+	long folds;
+	long Np;
+	long Nl;
+	long Nk;
+	long Ne;
+	long Nw;
+	long Ng;
+	long Nc;
+	long Nd;
+	int *weight_idxs;
+	double *ps;
+	double *lambdas;
+	double *kappas;
+	double *epsilons;
+	double *gammas;
+	double *coefs;
+	double *degrees;
+	char *train_data_file;
+	char *test_data_file;
+};
+
+// function declarations
+struct GenGrid *gensvm_init_grid();
+void gensvm_free_grid(struct GenGrid *grid);
+
+#endif
diff --git a/include/gensvm_gridsearch.h b/include/gensvm_gridsearch.h
new file mode 100644
index 0000000..dcd9b93
--- /dev/null
+++ b/include/gensvm_gridsearch.h
@@ -0,0 +1,37 @@
+/**
+ * @file gensvm_gridsearch.h
+ * @author Gertjan van den Burg
+ * @date August, 2013
+ * @brief Header file for gensvm_gridsearch.c
+ *
+ * @details
+ * The grid search for the optimal parameters is done through a queue.
+ * This file contains struct definitions for this queue and a single
+ * task in a queue, as well as a structure for the complete training
+ * scheme. Function declarations are also included.
+ *
+ */
+
+#ifndef GENSVM_GRIDSEARCH_H
+#define GENSVM_GRIDSEARCH_H
+
+// includes
+#include "gensvm_cv_util.h"
+#include "gensvm_init.h"
+#include "gensvm_grid.h"
+#include "gensvm_optimize.h"
+#include "gensvm_pred.h"
+#include "gensvm_queue.h"
+#include "gensvm_timer.h"
+
+// function declarations
+void gensvm_fill_queue(struct GenGrid *grid, struct GenQueue *queue,
+		struct GenData *train_data, struct GenData *test_data);
+void consistency_repeats(struct GenQueue *q, long repeats, TrainType traintype);
+void make_model_from_task(struct GenTask *task, struct GenModel *model);
+void print_progress_string(struct GenTask *task, long N);
+void start_training(struct GenQueue *q);
+double gensvm_cross_validation(struct GenModel *model,
+	       	struct GenData **train_folds, struct GenData **test_folds,
+		int folds, long n_total);
+#endif
diff --git a/include/gensvm_init.h b/include/gensvm_init.h
index 980366b..3f4a1cb 100644
--- a/include/gensvm_init.h
+++ b/include/gensvm_init.h
@@ -1,28 +1,21 @@
 /**
  * @file gensvm_init.h
  * @author Gertjan van den Burg
- * @date January, 2014
+ * @date May, 2016
  * @brief Header file for gensvm_init.c
  *
  * @details
- * Contains function declarations for the initialization functions for
- * GenModel and GenData structures.
+ * Contains function declarations for the initialization functions for the
+ * model weights and model V matrix.
  */
 
 #ifndef GENSVM_INIT_H
 #define GENSVM_INIT_H
 
-// include
-#include "globals.h"
-#include "gensvm.h"
+#include "gensvm_base.h"
 
-struct GenModel *gensvm_init_model();
-
-struct GenData *gensvm_init_data();
-
-void gensvm_allocate_model(struct GenModel *model);
-void gensvm_reallocate_model(struct GenModel *model, long n, long m);
-void gensvm_free_model(struct GenModel *model);
-void gensvm_free_data(struct GenData *data);
+void gensvm_init_V(struct GenModel *from_model, struct GenModel *to_model,
+		struct GenData *data);
+void gensvm_initialize_weights(struct GenData *data, struct GenModel *model);
 
 #endif
diff --git a/include/gensvm_io.h b/include/gensvm_io.h
index 4581c5f..9b0d973 100644
--- a/include/gensvm_io.h
+++ b/include/gensvm_io.h
@@ -12,9 +12,9 @@
 #ifndef GENSVM_IO_H
 #define GENSVM_IO_H
 
-// forward declarations
-struct GenData;
-struct GenModel;
+// includes
+#include "gensvm_base.h"
+#include "gensvm_strutil.h"
 
 // function declarations
 void gensvm_read_data(struct GenData *dataset, char *data_file);
@@ -24,5 +24,6 @@ void gensvm_write_model(struct GenModel *model, char *output_filename);
 
 void gensvm_write_predictions(struct GenData *data, long *predy,
 		char *output_filename);
+void gensvm_time_string(char *buffer);
 
 #endif
diff --git a/include/gensvm_kernel.h b/include/gensvm_kernel.h
index 45b7e62..a1fac20 100644
--- a/include/gensvm_kernel.h
+++ b/include/gensvm_kernel.h
@@ -14,12 +14,10 @@
 #ifndef GENSVM_KERNEL_H
 #define GENSVM_KERNEL_H
 
-// forward declarations
-struct GenData;
-struct GenModel;
+// includes
+#include "gensvm_base.h"
 
 // function declarations
-
 void gensvm_kernel_preprocess(struct GenModel *model, struct GenData *data);
 void gensvm_kernel_postprocess(struct GenModel *model,
 	       	struct GenData *traindata, struct GenData *testdata);
@@ -36,5 +34,9 @@ void gensvm_make_testfactor(struct GenData *testdata,
 double gensvm_dot_rbf(double *x1, double *x2, double *kernelparam, long n);
 double gensvm_dot_poly(double *x1, double *x2, double *kernelparam, long n);
 double gensvm_dot_sigmoid(double *x1, double *x2, double *kernelparam, long n);
-
+int dsyevx(char JOBZ, char RANGE, char UPLO, int N, double *A, int LDA,
+	       	double VL, double VU, int IL, int IU, double ABSTOL,
+		int *M, double *W, double *Z, int LDZ, double *WORK, int LWORK,
+		int *IWORK, int *IFAIL);
+double dlamch(char CMACH);
 #endif
diff --git a/include/gensvm_lapack.h b/include/gensvm_lapack.h
index c4e58e8..843169b 100644
--- a/include/gensvm_lapack.h
+++ b/include/gensvm_lapack.h
@@ -12,13 +12,4 @@
 #ifndef GENSVM_LAPACK_H
 #define GENSVM_LAPACK_H
 
-int dposv(char UPLO, int N, int NRHS, double *A, int LDA, double *B,
-		int LDB);
-int dsysv(char UPLO, int N, int NRHS, double *A, int LDA, int *IPIV,
-		double *B, int LDB, double *WORK, int LWORK);
-int dsyevx(char JOBZ, char RANGE, char UPLO, int N, double *A, int LDA,
-	       	double VL, double VU, int IL, int IU, double ABSTOL,
-		int *M, double *W, double *Z, int LDZ, double *WORK, int LWORK,
-		int *IWORK, int *IFAIL);
-double dlamch(char CMACH);
 #endif
diff --git a/include/gensvm_matrix.h b/include/gensvm_matrix.h
index 5c88f0b..9982b78 100644
--- a/include/gensvm_matrix.h
+++ b/include/gensvm_matrix.h
@@ -2,34 +2,15 @@
  * @file gensvm_matrix.h
  * @author Gertjan van den Burg
  * @date August, 2013
- * @brief Header file for gensvm_matrix.c
+ * @brief Header with defines for matrix access
  *
  * @details
- * Contains function declarations for functions useful for dealing with matrices.
+ * Contains defines useful for dealing with matrices.
  *
  */
 
 #ifndef GENSVM_MATRIX_H
 #define GENSVM_MATRIX_H
 
-// Set a matrix element (RowMajor)
-#define matrix_set(M, cols, i, j, val) M[(i)*(cols)+j] = val
-
-// Get a matrix element (RowMajor)
-#define matrix_get(M, cols, i, j) M[(i)*(cols)+j]
-
-// Add to a matrix element (RowMajor)
-#define matrix_add(M, cols, i, j, val) M[(i)*(cols)+j] += val
-
-// Multiply a matrix element (RowMajor)
-#define matrix_mul(M, cols, i, j, val) M[(i)*(cols)+j] *= val
-
-// Set a 3D matrix element (N2 = second dim, N3 = third dim, RowMajor)
-#define matrix3_set(M, N2, N3, i, j, k, val) M[k+(N3)*(j+(N2)*(i))] = val
-
-// Get a 3D matrix element (N2 = second dim, N3 = third dim, RowMajor)
-#define matrix3_get(M, N2, N3, i, j, k) M[k+(N3)*(j+(N2)*(i))]
-
-void print_matrix(double *M, long rows, long cols);
 
 #endif
diff --git a/include/gensvm_memory.h b/include/gensvm_memory.h
index bc4aae9..08d6f2d 100644
--- a/include/gensvm_memory.h
+++ b/include/gensvm_memory.h
@@ -9,6 +9,8 @@
 #ifndef GENSVM_MEMORY_H
 #define GENSVM_MEMORY_H
 
+#include <stddef.h>
+
 #define Calloc(type, size) \
 	mycalloc(__FILE__, __LINE__, size, sizeof(type))
 #define Malloc(type, size) \
diff --git a/include/gensvm_optimize.h b/include/gensvm_optimize.h
new file mode 100644
index 0000000..7a23bdb
--- /dev/null
+++ b/include/gensvm_optimize.h
@@ -0,0 +1,36 @@
+/**
+ * @file gensvm_train.h
+ * @author Gertjan van den Burg
+ * @date August, 2013
+ * @brief Header file for gensvm_train.c
+ *
+ * @details
+ * Contains function declarations for functions used to train a single
+ * GenModel.
+ *
+ */
+
+#ifndef GENSVM_TRAIN_H
+#define GENSVM_TRAIN_H
+
+#include "gensvm_sv.h"
+#include "gensvm_print.h"
+#include "gensvm_simplex.h"
+
+// function declarations
+void gensvm_optimize(struct GenModel *model, struct GenData *data);
+double gensvm_get_loss(struct GenModel *model, struct GenData *data,
+		double *ZV);
+void gensvm_get_update(struct GenModel *model, struct GenData *data,
+		double *B, double *ZAZ, double *ZAZV, double *ZAZVT);
+void gensvm_category_matrix(struct GenModel *model, struct GenData *data);
+void gensvm_simplex_diff(struct GenModel *model, struct GenData *dataset);
+void gensvm_calculate_errors(struct GenModel *model, struct GenData *data,
+	       	double *ZV);
+void gensvm_calculate_huber(struct GenModel *model);
+void gensvm_step_doubling(struct GenModel *model);
+int dposv(char UPLO, int N, int NRHS, double *A, int LDA, double *B, int LDB);
+int dsysv(char UPLO, int N, int NRHS, double *A, int LDA, int *IPIV, double *B,
+	       	int LDB, double *WORK, int LWORK);
+
+#endif
diff --git a/include/gensvm_pred.h b/include/gensvm_pred.h
index 97af01f..56e16e8 100644
--- a/include/gensvm_pred.h
+++ b/include/gensvm_pred.h
@@ -12,9 +12,9 @@
 #ifndef GENSVM_PRED_H
 #define GENSVM_PRED_H
 
-// forward declarations
-struct GenData;
-struct GenModel;
+// includes
+#include "gensvm_kernel.h"
+#include "gensvm_simplex.h"
 
 // function declarations
 void gensvm_predict_labels(struct GenData *testdata,
diff --git a/include/gensvm_print.h b/include/gensvm_print.h
new file mode 100644
index 0000000..fff7af5
--- /dev/null
+++ b/include/gensvm_print.h
@@ -0,0 +1,22 @@
+/**
+ * @file gensvm_print.h
+ * @author Gertjan van den Burg
+ * @date May, 2016
+ * @brief Header file for gensvm_print.c
+ *
+ * @details
+ * Function declarations for printing to stdout and stderr.
+ *
+ */
+
+#ifndef GENSVM_PRINT_H
+#define GENSVM_PRINT_H
+
+// includes
+#include "globals.h"
+
+// function declarations
+void note(const char *fmt,...);
+void err(const char *fmt,...);
+
+#endif
diff --git a/include/gensvm_queue.h b/include/gensvm_queue.h
new file mode 100644
index 0000000..e8d26d6
--- /dev/null
+++ b/include/gensvm_queue.h
@@ -0,0 +1,40 @@
+/**
+ * @file gensvm_queue.h
+ * @author Gertjan van den Burg
+ * @date August, 2013
+ * @brief Header file for gensvm_queue.c
+ *
+ * @details
+ * The grid search for the optimal parameters is done through a queue.
+ * This file contains struct definitions for this queue. Function declarations 
+ * for initializing and freeing the queue are also included.
+ *
+ */
+
+#ifndef GENSVM_QUEUE_H
+#define GENSVM_QUEUE_H
+
+#include "gensvm_task.h"
+
+/**
+ * @brief Simple task queue.
+ *
+ * This struct is basically just an array of pointers to Task instances,
+ * with a length and an index of the current task.
+ *
+ * @param **tasks 	array of pointers to Task structs
+ * @param N 		size of task array
+ * @param i 		index used for keeping track of the queue
+ */
+struct GenQueue {
+	struct GenTask **tasks;
+	long N;
+	long i;
+};
+
+// function declarations
+struct GenQueue *gensvm_init_queue();
+void gensvm_free_queue(struct GenQueue *q);
+struct GenTask *get_next_task(struct GenQueue *q);
+
+#endif
diff --git a/include/gensvm_simplex.h b/include/gensvm_simplex.h
new file mode 100644
index 0000000..9bb40b1
--- /dev/null
+++ b/include/gensvm_simplex.h
@@ -0,0 +1,18 @@
+/**
+ * @file gensvm_simplex.h
+ * @author Gertjan van den Burg
+ * @date May, 2016
+ * @brief Header file for gensvm_simplex.c
+ *
+ */
+
+#ifndef GENSVM_SIMPLEX_H
+#define GENSVM_SIMPLEX_H
+
+// includes
+#include "globals.h"
+
+// forward declarations
+void gensvm_simplex(long K, double *U);
+
+#endif
diff --git a/include/gensvm_strutil.h b/include/gensvm_strutil.h
index c51422f..efaa5ec 100644
--- a/include/gensvm_strutil.h
+++ b/include/gensvm_strutil.h
@@ -1,8 +1,8 @@
 /**
- * @file strutil.h
+ * @file gensvm_strutil.h
  * @author Gertjan van den Burg
  * @date August, 2013
- * @brief Header file for strutil.c
+ * @brief Header file for gensvm_strutil.c
  *
  * @details
  * Function declarations for useful string functions used in parsing
@@ -13,7 +13,7 @@
 #ifndef GENSVM_STRUTIL_H
 #define GENSVM_STRUTIL_H
 
-#include "types.h"
+#include "globals.h"
 
 bool str_startswith(const char *str, const char *pre);
 bool str_endswith(const char *str, const char *suf);
diff --git a/include/gensvm_sv.h b/include/gensvm_sv.h
index 2c7cf57..8347b95 100644
--- a/include/gensvm_sv.h
+++ b/include/gensvm_sv.h
@@ -12,6 +12,10 @@
 #ifndef GENSVM_SV_H
 #define GENSVM_SV_H
 
+// includes
+#include "gensvm_base.h"
+
+// function declarations
 long gensvm_num_sv(struct GenModel *model, struct GenData *data);
 
 #endif
diff --git a/include/gensvm_task.h b/include/gensvm_task.h
new file mode 100644
index 0000000..98c8f26
--- /dev/null
+++ b/include/gensvm_task.h
@@ -0,0 +1,53 @@
+/**
+ * @file gensvm_task.h
+ * @author Gertjan van den Burg
+ * @date August, 2013
+ * @brief Struct for a single task in the queue
+ *
+ * @details
+ * The grid search for the optimal parameters is done through a queue.
+ * This file contains struct definitions for the tasks in the queue.
+ * Initialization and free functions are also included.
+ *
+ */
+
+#ifndef GENSVM_TASK_H
+#define GENSVM_TASK_H
+
+#include "gensvm_base.h"
+
+/**
+ * @brief A structure for a single task in the queue.
+ *
+ * @param folds 	number of folds in cross validation
+ * @param ID 		numeric id of the task in the queue
+ * @param weight_idx 	parameter for the GenModel
+ * @param p 		parameter for the GenModel
+ * @param kappa 	parameter for the GenModel
+ * @param lambda 	parameter for the GenModel
+ * @param epsilon 	parameter for the GenModel
+ * @param kerneltype 	parameter for the GenModel
+ * @param *kernelparam parameters for the GenModel
+ * @param *train_data 	pointer to the training data
+ * @param *test_data 	pointer to the test data (if any)
+ * @param performance 	performance after cross validation
+ */
+struct GenTask {
+	KernelType kerneltype;
+	int weight_idx;
+	long folds;
+	long ID;
+	double p;
+	double kappa;
+	double lambda;
+	double epsilon;
+	double *kernelparam;
+	struct GenData *train_data;
+	struct GenData *test_data;
+	double performance;
+};
+
+struct GenTask *gensvm_init_task();
+void gensvm_free_task(struct GenTask *task);
+
+#endif
diff --git a/include/gensvm_timer.h b/include/gensvm_timer.h
index 29c45cd..11e61e5 100644
--- a/include/gensvm_timer.h
+++ b/include/gensvm_timer.h
@@ -12,8 +12,10 @@
 #ifndef GENSVM_TIMER_H
 #define GENSVM_TIMER_H
 
-double elapsed_time(clock_t s_time, clock_t e_time);
+// includes
+#include "globals.h"
 
-void get_time_string(char *buffer);
+// function declarations
+double gensvm_elapsed_time(clock_t s_time, clock_t e_time);
 
 #endif
diff --git a/include/gensvm_train.h b/include/gensvm_train.h
deleted file mode 100644
index 466b8e2..0000000
--- a/include/gensvm_train.h
+++ /dev/null
@@ -1,29 +0,0 @@
-/**
- * @file gensvm_train.h
- * @author Gertjan van den Burg
- * @date August, 2013
- * @brief Header file for gensvm_train.c
- *
- * @details
- * Contains function declarations for functions used to train a single
- * GenModel.
- *
- */
-
-#ifndef GENSVM_TRAIN_H
-#define GENSVM_TRAIN_H
-
-//forward declarations
-struct GenData;
-struct GenModel;
-
-// function declarations
-void gensvm_optimize(struct GenModel *model, struct GenData *data);
-
-double gensvm_get_loss(struct GenModel *model, struct GenData *data,
-		double *ZV);
-
-void gensvm_get_update(struct GenModel *model, struct GenData *data,
-		double *B, double *ZAZ, double *ZAZV, double *ZAZVT);
-
-#endif
diff --git a/include/gensvm_train_dataset.h b/include/gensvm_train_dataset.h
deleted file mode 100644
index 9a3fe86..0000000
--- a/include/gensvm_train_dataset.h
+++ /dev/null
@@ -1,143 +0,0 @@
-/**
- * @file gensvm_train_dataset.h
- * @author Gertjan van den Burg
- * @date August, 2013
- * @brief Structs and functions necessary for the grid search
- *
- * @details
- * The grid search for the optimal parameters is done through a queue.
- * This file contains struct definitions for this queue and a single
- * task in a queue, as well as a structure for the complete training
- * scheme. Function declarations are also included.
- *
- */
-
-#ifndef GENSVM_TRAIN_DATASET_H
-#define GENSVM_TRAIN_DATASET_H
-
-#include "types.h"
-
-// forward declarations
-struct GenData;
-struct GenModel;
-
-/**
- * @brief A structure for a single task in the queue.
- *
- * @param folds 	number of folds in cross validation
- * @param ID 		numeric id of the task in the queue
- * @param weight_idx 	parameter for the GenModel
- * @param p 		parameter for the GenModel
- * @param kappa 	parameter for the GenModel
- * @param lambda 	parameter for the GenModel
- * @param epsilon 	parameter for the GenModel
- * @param kerneltype 	parameter for the GenModel
- * @param *kernelparam parameters for the GenModel
- * @param *train_data 	pointer to the training data
- * @param *test_data 	pointer to the test data (if any)
- * @param performance 	performance after cross validation
- */
-struct Task {
-	KernelType kerneltype;
-	int weight_idx;
-	long folds;
-	long ID;
-	double p;
-	double kappa;
-	double lambda;
-	double epsilon;
-	double *kernelparam;
-	struct GenData *train_data;
-	struct GenData *test_data;
-	double performance;
-};
-
-/**
- * @brief Simple task queue.
- *
- * This struct is basically just an array of pointers to Task instances,
- * with a length and an index of the current task.
- *
- * @param **tasks 	array of pointers to Task structs
- * @param N 		size of task array
- * @param i 		index used for keeping track of the queue
- */
-struct Queue {
-	struct Task **tasks;
-	long N;
-	long i;
-};
-
-/**
- * @brief Structure for describing the entire grid search
- *
- * @param traintype 		type of training to use
- * @param kerneltype 		type of kernel to use throughout training
- * @param repeats 		number of repeats to be done after the grid
- * 				search to find the parameter set with the
- * 				most consistent high performance
- * @param folds 		number of folds in cross validation
- * @param Np 			size of the array of p values
- * @param Nl 			size of the array of lambda values
- * @param Nk 			size of the array of kappa values
- * @param Ne 			size of the array of epsilon values
- * @param Nw 			size of the array of weight_idx values
- * @param Ng 			size of the array of gamma values
- * @param Nc 			size of the array of coef values
- * @param Nd 			size of the array of degree values
- * @param *weight_idxs 		array of weight_idxs
- * @param *ps 			array of p values
- * @param *lambdas 		array of lambda values
- * @param *kappas 		array of kappa values
- * @param *epsilons 		array of epsilon values
- * @param *gammas 		array of gamma values
- * @param *coefs 		array of coef values
- * @param *degrees 		array of degree values
- * @param *train_data_file 	filename of train data file
- * @param *test_data_file 	filename of test data file
- *
- */
-struct Training {
-	TrainType traintype;
-	KernelType kerneltype;
-	long repeats;
-	long folds;
-	long Np;
-	long Nl;
-	long Nk;
-	long Ne;
-	long Nw;
-	long Ng;
-	long Nc;
-	long Nd;
-	int *weight_idxs;
-	double *ps;
-	double *lambdas;
-	double *kappas;
-	double *epsilons;
-	double *gammas;
-	double *coefs;
-	double *degrees;
-	char *train_data_file;
-	char *test_data_file;
-};
-
-void make_queue(struct Training *training, struct Queue *queue,
-		struct GenData *train_data, struct GenData *test_data);
-
-struct Task *get_next_task(struct Queue *q);
-void free_queue(struct Queue *q);
-
-void consistency_repeats(struct Queue *q, long repeats, TrainType traintype);
-
-void make_model_from_task(struct Task *task, struct GenModel *model);
-void copy_model(struct GenModel *from, struct GenModel *to);
-
-void print_progress_string(struct Task *task, long N);
-
-// new
-void start_training(struct Queue *q);
-double gensvm_cross_validation(struct GenModel *model,
-	       	struct GenData **train_folds, struct GenData **test_folds,
-		int folds, long n_total);
-#endif
diff --git a/include/gensvm_util.h b/include/gensvm_util.h
deleted file mode 100644
index 5ea2198..0000000
--- a/include/gensvm_util.h
+++ /dev/null
@@ -1,26 +0,0 @@
-/**
- * @file util.h
- * @author Gertjan van den Burg
- * @date August, 2013
- * @brief Header file for util.c
- *
- * @details
- * Function declarations for utility functions of the program.
- *
- */
-
-#ifndef GENSVM_UTIL_H
-#define GENSVM_UTIL_H
-
-// forward declarations
-struct GenData;
-struct GenModel;
-
-// function declarations
-int gensvm_check_argv(int argc, char **argv, char *str);
-int gensvm_check_argv_eq(int argc, char **argv, char *str);
-
-void note(const char *fmt,...);
-void err(const char *fmt,...);
-
-#endif
diff --git a/include/globals.h b/include/globals.h
index becde35..7fad7b1 100644
--- a/include/globals.h
+++ b/include/globals.h
@@ -18,12 +18,17 @@
 #ifndef GENSVM_GLOBALS_H
 #define GENSVM_GLOBALS_H
 
+#include "gensvm_memory.h"
+#include "types.h"
+
+#include <stdarg.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <stdbool.h>
 #include <string.h>
-
-#include "gensvm_memory.h"
+#include <math.h>
+#include <time.h>
+#include <cblas.h>
 
 #define MAX_LINE_LENGTH 1024
 
@@ -33,4 +38,22 @@
 #define minimum(a, b) (a) < (b) ? (a) : (b)
 #endif
 
+// Set a matrix element (RowMajor)
+#define matrix_set(M, cols, i, j, val) M[(i)*(cols)+j] = val
+
+// Get a matrix element (RowMajor)
+#define matrix_get(M, cols, i, j) M[(i)*(cols)+j]
+
+// Add to a matrix element (RowMajor)
+#define matrix_add(M, cols, i, j, val) M[(i)*(cols)+j] += val
+
+// Multiply a matrix element (RowMajor)
+#define matrix_mul(M, cols, i, j, val) M[(i)*(cols)+j] *= val
+
+// Set a 3D matrix element (N2 = second dim, N3 = third dim, RowMajor)
+#define matrix3_set(M, N2, N3, i, j, k, val) M[k+(N3)*(j+(N2)*(i))] = val
+
+// Get a 3D matrix element (N2 = second dim, N3 = third dim, RowMajor)
+#define matrix3_get(M, N2, N3, i, j, k) M[k+(N3)*(j+(N2)*(i))]
+
 #endif
diff --git a/include/libGenSVM.h b/include/libGenSVM.h
index 9e2d4c2..146fc67 100644
--- a/include/libGenSVM.h
+++ b/include/libGenSVM.h
@@ -23,7 +23,6 @@ struct GenData;
 struct GenModel;
 
 // function declarations
-void gensvm_simplex_gen(long K, double *U);
 void gensvm_category_matrix(struct GenModel *model, struct GenData *data);
 void gensvm_simplex_diff(struct GenModel *model, struct GenData *dataset);
 
@@ -33,8 +32,5 @@ void gensvm_calculate_huber(struct GenModel *model);
 
 void gensvm_step_doubling(struct GenModel *model);
 
-void gensvm_seed_model_V(struct GenModel *from_model,
-	       	struct GenModel *to_model, struct GenData *data);
-void gensvm_initialize_weights(struct GenData *data, struct GenModel *model);
 
 #endif